[CP2K:10240] Re: rewrite cp2k cube file for Henkelman's code

[Matt W]

The code is

         IF (dft_control%qs_control%gapw) THEN
            CALL pw_transfer(rho0_s_gs%pw, wf_r%pw)
            IF (dft_control%qs_control%gapw_control%nopaw_as_gpw) THEN
               CALL pw_axpy(rho_core%pw, wf_r%pw)
            END IF
         ELSE
            CALL pw_transfer(rho_core%pw, wf_r%pw)
         END IF


So for GPW it will add in a Gaussian charge with value +Zeffective centred 
on the atoms the same as is done when calculating electrostatics (see 
original paper).

It is quite possible to post process the results of a trajectory to add in 
an atom centred density.

Matt

On Tuesday, May 1, 2018 at 8:54:09 PM UTC+1, Ada Sedova wrote:
>
> Right- I know you said that. The response from David didn't seem to relate 
> to the original question. You also said you hadn't tried it. The link to 
> the cp2k forum discussion I added above shows that it does not in fact add 
> it, if you are not using GAPW.
>
> So, the question is, does it add it or not? It seems from the above, it 
> does not. Someone familiar with the code would have to determine if this is 
> true or not. For me, I have tens of picoseconds of simulation for systems 
> with hundred of atoms, and re-running this to check would be a pain. I 
> would do it if I knew for sure it would work. I'm trying to monitor the 
> changing densities.
>
>  
>
> On Tue, May 1, 2018 at 1:21 PM, Matt W <matt... at gmail.com <javascript:>> 
> wrote:
>
>> According to Matt, just running with the TOTAL...etc command will add the 
>>> core electrons. Are you saying this works? Because a previous thread, 
>>> linked above, describes this as not working unless you are using GAPW, not 
>>> just GPW.
>>>
>>>
>> Hi Ada,
>>
>> no, I said it would a add in a core charge at the nuclei equal to the Z 
>> effective of the pseudo at the atom centre. 
>>
>> What is required for getting a correct topological description to get AIM 
>> descriptors? I haven't read up on it.
>>
>> Adding in an atomic density that does not respond to the valence density 
>> could be made into a fairly simple post-processing step - is that what is 
>> needed, the [core] atom density (from an isolated atom) added to the 
>> density cube file?
>>
>> Matt
>>  
>>
>>  
>>
>>> -Ada
>>>
>>>
>>>
>>> On Tue, May 1, 2018 at 9:33 AM, David T <amazi... at gmail.com> wrote:
>>>
>>>> You are right Matt.
>>>> I did it for the 1st time in this article: 
>>>> https://pubs.acs.org/doi/abs/10.1021/jp901753p
>>>>
>>>> Sadly Henkelman and VASP persons have started using my Algorithm 
>>>> without citing it... but that is another story....
>>>>
>>>>
>>>> On Tuesday, 17 April 2018 19:19:13 UTC+1, Matt W wrote:
>>>>>
>>>>> I _think_ it should add the approximate core charge for GPW (i.e. a 
>>>>> gaussian with charge +Z centred on the atom), which should be enough for 
>>>>> the correct topology for AIM. 
>>>>>
>>>>> I'm not speaking from experience though. May well be wrong.
>>>>>
>>>>> On Tuesday, April 17, 2018 at 7:08:09 PM UTC+1, Ada Sedova wrote:
>>>>>>
>>>>>> I think that only works if you're using GAPW, though, am I right? 
>>>>>> Because if you are not calculating the core electrons they won't print? At 
>>>>>> least that's according to another thread I read on this forum...
>>>>>>
>>>>>> On Tue, Apr 17, 2018 at 12:49 PM, Matt W <matt... at gmail.com> wrote:
>>>>>>
>>>>>>>
>>>>>>> https://manual.cp2k.org/cp2k-5_1-branch/CP2K_INPUT/FORCE_EVAL/DFT/PRINT/TOT_DENSITY_CUBE.html
>>>>>>>
>>>>>>> I think.
>>>>>>>
>>>>>>> On Tuesday, April 17, 2018 at 5:14:12 PM UTC+1, Ada Sedova wrote:
>>>>>>>>
>>>>>>>> Hi all-
>>>>>>>> There was a thread from 2016 about finding a way to add core 
>>>>>>>> electrons to a cp2k cube file so that Bader analysis can be performed with 
>>>>>>>> Henkelman's code, which takes cube files, but of the Gaussian format, which 
>>>>>>>> includes all electrons. There was no definitive solution posted, but a 
>>>>>>>> suggestion was to hack the Manz DDEC code to add core electrons and print 
>>>>>>>> out a new cube. The Manz code has gone through some changes and a brief 
>>>>>>>> look at it did not reveal a rewrite option. 
>>>>>>>>
>>>>>>>> I was wondering if there have been any updates on the ability to 
>>>>>>>> use Henkelman's with a cp2k cube file. The other option would be to create 
>>>>>>>> a VASP CHGCAR file from a cp2k cube file, but the core electrons still need 
>>>>>>>> to be added somehow.
>>>>>>>>
>>>>>>>> Thanks!
>>>>>>>> AS
>>>>>>>>
>>>>>>> -- 
>>>>>>> You received this message because you are subscribed to a topic in 
>>>>>>> the Google Groups "cp2k" group.
>>>>>>> To unsubscribe from this topic, visit 
>>>>>>> https://groups.google.com/d/topic/cp2k/IVj1WAxCAYs/unsubscribe.
>>>>>>> To unsubscribe from this group and all its topics, send an email to 
>>>>>>> cp2k+... at googlegroups.com.
>>>>>>> To post to this group, send email to cp... at googlegroups.com.
>>>>>>> Visit this group at https://groups.google.com/group/cp2k.
>>>>>>> For more options, visit https://groups.google.com/d/optout.
>>>>>>>
>>>>>>
>>>>>> -- 
>>>> You received this message because you are subscribed to a topic in the 
>>>> Google Groups "cp2k" group.
>>>> To unsubscribe from this topic, visit 
>>>> https://groups.google.com/d/topic/cp2k/IVj1WAxCAYs/unsubscribe.
>>>> To unsubscribe from this group and all its topics, send an email to 
>>>> cp2k+... at googlegroups.com.
>>>> To post to this group, send email to cp... at googlegroups.com.
>>>> Visit this group at https://groups.google.com/group/cp2k.
>>>> For more options, visit https://groups.google.com/d/optout.
>>>>
>>>
>>> -- 
>> You received this message because you are subscribed to a topic in the 
>> Google Groups "cp2k" group.
>> To unsubscribe from this topic, visit 
>> https://groups.google.com/d/topic/cp2k/IVj1WAxCAYs/unsubscribe.
>> To unsubscribe from this group and all its topics, send an email to 
>> cp2k+... at googlegroups.com <javascript:>.
>> To post to this group, send email to cp... at googlegroups.com <javascript:>
>> .
>> Visit this group at https://groups.google.com/group/cp2k.
>> For more options, visit https://groups.google.com/d/optout.
>>
>
>
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://lists.cp2k.org/archives/cp2k-user/attachments/20180501/ae18796b/attachment.htm>